That model uses a 59 (SH-N1) at the neck and a Custom (SH-5) at the bridge. I use a 59 at the neck position on 4 of my guitars and have been satisfied. Take a look at the Seymour Duncan link below. There are sound bites that you might be able to make comparisons with. What are you using for an amp and are you using any effect devices? I'm just curious about what other factors might exist.

Yah, drop the height. Too many (sorry) ****ers put the poles within 2mm (or less!) of the strings, figuring they'll get more volume or power or sustain or wtfever the current buzz-word is. Well, they do get it, at the cost of tonal coloration. I've had a few customers that I could've gotten to pay me for replacing their pickups, when all I did was give the screws a few turns -- but, I at least attempt to be honest.

If the pickups were installed aftermarket, then it's possible there's a tone-knob short & a capacitor is stealing high tones.

If that doesn't help, then consider "cooler" pickups (lower ohmage) or speak to a winder about changing your magnets.

I have the same issue with mine! Even if I roll off the volume I don't get the clarity I would have hoped for. It's a shame because it stops me playing the guitar. I love how it feels and how it plays but have never been happy with the sound. I think I'll take a look at the pickup height and see if they need to be lowered!